[gmx-users] g_hbond

[sulatha M. S]

As suggested by David I extended the simulations (total of 25ns) for a
single chain polyacid in 5500 water molecules and tried to calculate the
H-bond ACF. I get the same negative lifetime for Hbonds between COOH groups
and water. Is it that the g_hbond ACF giving weird results for this case.
For chains with COO- and COOH groups (50% each), I got positive life times
of Hbond. Ayy ideas on how to solve this will be of great help. I am using
4.0.7 version. The command line I gave was
g_hbond -f traj.xtc -s traj.tpr -n index.ndx -ac and chose the polyacid and
the water as  the two groups.


ACF 22057/22057
Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0146697
Q =          0
------------------------------
--------------------
Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward        -0.271     -3.687    -666.000   0.0146697
Backward       -2.291     -0.437    -666.000
One-way         0.101      9.882      10.207
Integral        0.034     29.376      12.907
Relaxation      0.063     15.803      11.370


Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India


On Tue, Dec 13, 2011 at 10:12 AM, sulatha M. S <mssulatha at gmail.com> wrote:

>
>
> I did not get a warning here. I also have simulations (20ns) of
>>> copolyacids where again it gave me negative life time. These runs are
>>> well equilibrated with respect to energy and Rg of the polymers. The
>>> system is a 20 repeat unit chain in approx. 5500 water molecules. I have
>>> done simulations in which 10 units are COO- and the remaining 10 as COOH
>>> along the chain. With a 10ns trajectory, the average life time of
>>> H-bonds is positive.Only in the case of unionized acid I am getting a
>>> negative life time.
>>>
>>>  Did you look at the ACF graph? It could be constant at 1 or 0.
>>
>
> Yes, the ACF decays to 0 and remains constant in all cases
>
>
>
>>
>>>
>>>    Thankyou for any help,
>>>
>>>    Dr. M. S. Sulatha
>>>    Dept. of Chemical Engineering
>>>    IIT-Madras
>>>    India
>>>
>>>
>>>
>>>
>>>    --
>>>    David van der Spoel, Ph.D., Professor of Biology
>>>    Dept. of Cell & Molec. Biol., Uppsala University.
>>>    Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>    spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>>>
>>>    http://folding.bmc.uu.se
>>>    --
>>>    gmx-users mailing list gmx-users at gromacs.org
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>>>    What is the value for free energy of H-bonding.
>>>
>>>
>>>
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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>
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